moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / ordervector.cpp

diff --git a/ordervector.cpp b/ordervector.cpp
deleted file mode 100644 (file)
index a6dff32..0000000
--- a/ordervector.cpp
+++ /dev/null
@@ -1,244 +0,0 @@
-/*
- *  order.cpp
- *  
- *
- *  Created by Pat Schloss on 8/8/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "ordervector.hpp"
-
-
-/***********************************************************************/
-
-OrderVector::OrderVector() : DataVector() {}
-
-/***********************************************************************/
-
-//OrderVector::OrderVector(int ns) : DataVector(), data(ns, -1) {}
-
-/***********************************************************************/
-
-OrderVector::OrderVector(string id, vector<int> ov) : 
-                                                                                       DataVector(id), data(ov)
-{
-       updateStats();  
-}
-
-/***********************************************************************/
-
-OrderVector::OrderVector(ifstream& f) : DataVector() {
-       try {
-               int hold;
-       
-               f >> label;
-               f >> hold;
-       
-               data.assign(hold, -1);
-       
-               int inputData;
-       
-               for(int i=0;i<hold;i++){
-                       f >> inputData;
-                       set(i, inputData);
-               }
-       
-               updateStats();
-       }
-       catch(exception& e) {
-               m->errorOut(e, "OrderVector", "OrderVector");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-
-int OrderVector::getNumBins(){
-       if(needToUpdate == 1){  updateStats();  }
-       return numBins;
-}
-
-/***********************************************************************/
-
-int OrderVector::getNumSeqs(){
-       if(needToUpdate == 1){  updateStats();  }
-       return numSeqs;
-}
-
-/***********************************************************************/
-
-int OrderVector::getMaxRank(){
-       if(needToUpdate == 1){  updateStats();  }
-       return maxRank;
-}
-/***********************************************************************/
-
-void OrderVector::clear(){
-       numBins = 0;
-       maxRank = 0;
-       numSeqs = 0;
-       data.clear();
-}
-/***********************************************************************/
-
-
-
-void OrderVector::set(int index, int binNumber){
-       
-       data[index] = binNumber;
-       needToUpdate = 1;
-       
-}
-
-/***********************************************************************/
-
-int OrderVector::get(int index){
-       return data[index];                     
-}
-
-/***********************************************************************/
-
-void OrderVector::push_back(int index){
-
-       data.push_back(index);
-       needToUpdate = 1;
-       
-}
-
-/***********************************************************************/
-
-void OrderVector::print(ostream& output){
-       try {
-               output << label << '\t' << numSeqs << '\t';
-       
-               for(int i=0;i<data.size();i++){
-                       output << data[i] << '\t';
-               }
-               output << endl;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "OrderVector", "print");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-void OrderVector::print(string prefix, ostream& output){
-       try {
-               output << prefix << '\t' << numSeqs << '\t';
-       
-               for(int i=0;i<numSeqs;i++){
-                       output << data[i] << '\t';
-               }
-               output << endl;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "OrderVector", "print");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-void OrderVector::resize(int){
-       m->mothurOut("resize() did nothing in class OrderVector");
-}
-
-/***********************************************************************/
-
-int OrderVector::size(){
-       return data.size();                                     
-}
-
-/***********************************************************************/
-
-vector<int>::iterator OrderVector::begin(){
-       return data.begin();    
-}
-
-/***********************************************************************/
-
-vector<int>::iterator OrderVector::end(){
-       return data.end();              
-}
-
-/***********************************************************************/
-
-RAbundVector OrderVector::getRAbundVector(){
-       try {
-               RAbundVector rav(data.size());
-       
-               for(int i=0;i<numSeqs;i++){
-                       rav.set(data[i], rav.get(data[i]) + 1);
-               }       
-               sort(rav.rbegin(), rav.rend());
-               for(int i=numSeqs-1;i>=0;i--){
-                       if(rav.get(i) == 0){    rav.pop_back(); }
-                       else{
-                               break;
-                       }
-               }
-               rav.setLabel(label);
-
-               return rav;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "OrderVector", "getRAbundVector");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-SAbundVector OrderVector::getSAbundVector(){
-       
-       RAbundVector rav(this->getRAbundVector());
-       return rav.getSAbundVector();
-
-}
-
-/***********************************************************************/
-
-OrderVector OrderVector::getOrderVector(map<string,int>* hold = 0){
-       return *this;                   
-}
-
-/***********************************************************************/
-
-void OrderVector::updateStats(){
-       try {
-               needToUpdate = 0;
-       //      int maxBinVectorLength = 0;
-               numSeqs = 0;
-               numBins = 0;
-               maxRank = 0;
-       
-               for(int i=0;i<data.size();i++){
-                       if(data[i] != -1){
-                               numSeqs++;
-                       }
-               }
-       
-               vector<int> hold(numSeqs);
-       
-               for(int i=0;i<numSeqs;i++){
-                       if(data[i] != -1){
-                               hold[data[i]] = hold[data[i]]+1;
-                       }
-               }       
-               for(int i=0;i<numSeqs;i++){
-                       if(hold[i] > 0)                 {       numBins++;                      }
-                       if(hold[i] > maxRank)   {       maxRank = hold[i];      }
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "OrderVector", "updateStats");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-